2026-07-27T01:43:21,394 Created temporary directory: /tmp/pip-ephem-wheel-cache-ui23foxw
2026-07-27T01:43:21,396 Created temporary directory: /tmp/pip-build-tracker-yfpmql1q
2026-07-27T01:43:21,397 Initialized build tracking at /tmp/pip-build-tracker-yfpmql1q
2026-07-27T01:43:21,397 Created build tracker: /tmp/pip-build-tracker-yfpmql1q
2026-07-27T01:43:21,398 Entered build tracker: /tmp/pip-build-tracker-yfpmql1q
2026-07-27T01:43:21,398 Created temporary directory: /tmp/pip-wheel-62xu9xnm
2026-07-27T01:43:21,401 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-07-27T01:43:21,404 Created temporary directory: /tmp/pip-ephem-wheel-cache-5l_vq8s8
2026-07-27T01:43:21,425 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-27T01:43:21,428 2 location(s) to search for versions of shephard:
2026-07-27T01:43:21,428 * https://pypi.org/simple/shephard/
2026-07-27T01:43:21,428 * https://www.piwheels.org/simple/shephard/
2026-07-27T01:43:21,429 Fetching project page and analyzing links: https://pypi.org/simple/shephard/
2026-07-27T01:43:21,430 Getting page https://pypi.org/simple/shephard/
2026-07-27T01:43:21,431 Found index url https://pypi.org/simple
2026-07-27T01:43:21,726 Fetched page https://pypi.org/simple/shephard/ as application/vnd.pypi.simple.v1+json
2026-07-27T01:43:21,730   Found link https://files.pythonhosted.org/packages/a9/95/cbdbdeb72c0c4970872dc8b61c9df622274cc80602640b478e234c921234/shephard-0.1.5.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.5
2026-07-27T01:43:21,730   Found link https://files.pythonhosted.org/packages/e9/11/69a637d6d4e0cb3a2addc9c06587e781747dfee014076fdaab76d466c46f/shephard-0.1.7.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.7
2026-07-27T01:43:21,731   Found link https://files.pythonhosted.org/packages/b7/90/ea0b27088b3586d48ecaaae9743f8289d28c8e602c4aee5bb4e342b06fc5/shephard-0.1.8.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.8
2026-07-27T01:43:21,732   Found link https://files.pythonhosted.org/packages/2d/0b/2c408626a7f199cb04f61d0fffb3372420ad5564e6bffb942646d140232a/shephard-0.1.12.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.12
2026-07-27T01:43:21,733   Found link https://files.pythonhosted.org/packages/60/78/e58f5c608c7cc8363648b8466f262582a7de95a0331f7b3e87085cf31179/shephard-0.1.14.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.14
2026-07-27T01:43:21,733   Found link https://files.pythonhosted.org/packages/78/01/9fc9805f42e59bdf8a00197d349471405e1f27c254562ef81a79f0c67a18/shephard-0.1.15.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.15
2026-07-27T01:43:21,734   Found link https://files.pythonhosted.org/packages/c6/9c/5920ae7fe8ea8af0aa79d7d2554018f6408462d68ac30b501933c9870bc9/shephard-0.1.16.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.16
2026-07-27T01:43:21,735   Found link https://files.pythonhosted.org/packages/b9/7c/03b2d14b68bd74d6dbdef3acd2a59faa9eebb74bc9b5bd623488ae60bf0c/shephard-0.1.17.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.17
2026-07-27T01:43:21,736   Found link https://files.pythonhosted.org/packages/78/a1/eda32772db5f73f89f29c1827f159ee9715a2adb6c0cd7d4d8272fde7c0a/shephard-0.1.20.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7,<3.12.0), version: 0.1.20
2026-07-27T01:43:21,737   Found link https://files.pythonhosted.org/packages/1d/74/63cf0dc536cee0215cdee8ea059f7fa2207748646d24e93de829ac0f9b1f/shephard-0.1.21.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7,<3.12.0), version: 0.1.21
2026-07-27T01:43:21,738   Found link https://files.pythonhosted.org/packages/68/39/e27dc8f28f0b456c82c497b702bf945bc6596ccf72665cbfe873ecfbcc58/shephard-0.2.0.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7), version: 0.2.0
2026-07-27T01:43:21,739   Found link https://files.pythonhosted.org/packages/5f/73/f7cd4bfd9dda99aec6247051206598c1cf2684faca7b90a06660a540ab1f/shephard-0.2.1.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7), version: 0.2.1
2026-07-27T01:43:21,740   Found link https://files.pythonhosted.org/packages/f8/16/aa35d7ab6fa18f8b58edb4213a080f01f43ce1c3ec87ddb4ab533601cdaf/shephard-0.2.2.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7), version: 0.2.2
2026-07-27T01:43:21,741   Skipping link: No binaries permitted for shephard: https://files.pythonhosted.org/packages/d6/f5/a3e2a50fccff77e44759d1866b05d689ebb92ec62b5998a5cfe844196a04/shephard-0.2.3-py3-none-any.whl (from https://pypi.org/simple/shephard/) (requires-python:>=3.10)
2026-07-27T01:43:21,741   Found link https://files.pythonhosted.org/packages/08/b2/7df159885a6ad070ae8a733f96d4fb9a760ee784124ae03db919458e63bc/shephard-0.2.3.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.10), version: 0.2.3
2026-07-27T01:43:21,742   Skipping link: No binaries permitted for shephard: https://files.pythonhosted.org/packages/fb/ff/81b203ad8c88fdf57649b15994bdf04aabd9276e85205374749450e2a660/shephard-0.2.4-py3-none-any.whl (from https://pypi.org/simple/shephard/) (requires-python:>=3.10)
2026-07-27T01:43:21,743   Found link https://files.pythonhosted.org/packages/4e/a8/d92e021bf1cb6842f6a5b9f2afedcd6ce0f76af18564ff5f0f616b0561eb/shephard-0.2.4.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.10), version: 0.2.4
2026-07-27T01:43:21,743 Fetching project page and analyzing links: https://www.piwheels.org/simple/shephard/
2026-07-27T01:43:21,744 Getting page https://www.piwheels.org/simple/shephard/
2026-07-27T01:43:21,745 Found index url https://www.piwheels.org/simple
2026-07-27T01:43:21,927 Fetched page https://www.piwheels.org/simple/shephard/ as text/html
2026-07-27T01:43:21,933   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.2.3-py3-none-any.whl#sha256=5fc4d758d03e293d2abeca08ccf2b5d9d36ecdd842c63c24b5920ac46342b2de (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.10)
2026-07-27T01:43:21,933   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/SHEPHARD-0.2.2-py3-none-any.whl#sha256=439b7a735d0a7049a0e6221661fc776137c9e179ad5f2a320e5392bb8069f20b (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7)
2026-07-27T01:43:21,934   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/SHEPHARD-0.2.1-py3-none-any.whl#sha256=c2938ecde6fe46680cbd7eaeaaac9786f78306fc45827bc64fc01bacedebf1aa (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7)
2026-07-27T01:43:21,935   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/SHEPHARD-0.2.0-py3-none-any.whl#sha256=bf25de7957cfc8245aa838a5f45de3b9493736e1329249b856aca74b167a11d2 (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7)
2026-07-27T01:43:21,935   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.21-py3-none-any.whl#sha256=a7b74868e7b3d7a863c6bcb667f0f6e90071dfcfc14fedffb0f42d538e6cb261 (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7,<3.12.0)
2026-07-27T01:43:21,936   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.20-py3-none-any.whl#sha256=24e0e6400e28f09571d88701fe01ae333e945fde39dac06662db18acf07102f7 (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7,<3.12.0)
2026-07-27T01:43:21,936   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.17-py3-none-any.whl#sha256=e58970e02d8a29858bffaa02f2b81a682a9ff647ab2d40add23077b69f3ac021 (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,937   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.16-py3-none-any.whl#sha256=f8e78c819d4b0150399cc6bb2176f78cba05e409f65559ce80fd765577c27f81 (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,938   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.15-py3-none-any.whl#sha256=79ddd35e1cf2c5fc12afbbb7ccd13a338a58db5b7af8b2777c70a6ec6c6a5e6f (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,938   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.14-py3-none-any.whl#sha256=475a3c0e8212f4d337f0f1dc4abe953595d119c3b46c8cc25fcc63502c39ac2d (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,938   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.12-py3-none-any.whl#sha256=11352de9001ada56ef480863bdad4b36727295a16dfd6bdbbb8b4c13523d07ba (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,939   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.8-py3-none-any.whl#sha256=affda4c08aba9e71908aa718a3fdb9851faff0a49135550c7741cbeb0d804582 (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,939   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.7-py3-none-any.whl#sha256=e515f924da74d106bd56b75ebb3d14350dfd59ecae19d4004c155b7894558ee9 (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,940   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.5-py3-none-any.whl#sha256=920236db73af811e8085b5527ca1713d3434695a2dc7a8a4da603b7034a40f67 (from https://www.piwheels.org/simple/shephard/)
2026-07-27T01:43:21,940 Skipping link: not a file: https://www.piwheels.org/simple/shephard/
2026-07-27T01:43:21,941 Skipping link: not a file: https://pypi.org/simple/shephard/
2026-07-27T01:43:21,962 Given no hashes to check 1 links for project 'shephard': discarding no candidates
2026-07-27T01:43:21,981 Collecting shephard==0.2.4
2026-07-27T01:43:21,984   Created temporary directory: /tmp/pip-unpack-pfg77ydy
2026-07-27T01:43:22,130   Downloading shephard-0.2.4.tar.gz (230 kB)
2026-07-27T01:43:22,451   Added shephard==0.2.4 from https://files.pythonhosted.org/packages/4e/a8/d92e021bf1cb6842f6a5b9f2afedcd6ce0f76af18564ff5f0f616b0561eb/shephard-0.2.4.tar.gz to build tracker '/tmp/pip-build-tracker-yfpmql1q'
2026-07-27T01:43:22,459   Created temporary directory: /tmp/pip-build-env-5i7e5g__
2026-07-27T01:43:22,463   Installing build dependencies: started
2026-07-27T01:43:22,464   Running command pip subprocess to install build dependencies
2026-07-27T01:43:23,661   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-07-27T01:43:24,086   DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-07-27T01:43:24,111   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-27T01:43:25,869   Collecting setuptools>=77
2026-07-27T01:43:25,870     Obtaining dependency information for setuptools>=77 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata
2026-07-27T01:43:25,884     Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB)
2026-07-27T01:43:26,007   Collecting versioningit~=2.0
2026-07-27T01:43:26,008     Obtaining dependency information for versioningit~=2.0 from https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl.metadata
2026-07-27T01:43:26,206     Downloading https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl.metadata (9.4 kB)
2026-07-27T01:43:26,410   Collecting packaging>=17.1
2026-07-27T01:43:26,410     Obtaining dependency information for packaging>=17.1 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-07-27T01:43:26,423     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-07-27T01:43:26,618   Downloading https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl (35 kB)
2026-07-27T01:43:26,647   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-27T01:43:26,739   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-27T01:43:26,778   Using cached https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl (35 kB)
2026-07-27T01:43:26,803   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-27T01:43:26,885   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-27T01:43:29,645   Installing collected packages: setuptools, packaging, versioningit
2026-07-27T01:43:33,031     Creating /tmp/pip-build-env-5i7e5g__/overlay/local/bin
2026-07-27T01:43:33,033     changing mode of /tmp/pip-build-env-5i7e5g__/overlay/local/bin/versioningit to 755
2026-07-27T01:43:33,055   Successfully installed packaging-26.2 setuptools-83.0.0 versioningit-2.3.0
2026-07-27T01:43:33,341   Installing build dependencies: finished with status 'done'
2026-07-27T01:43:33,348   Getting requirements to build wheel: started
2026-07-27T01:43:33,349   Running command Getting requirements to build wheel
2026-07-27T01:43:34,079   running egg_info
2026-07-27T01:43:34,085   writing SHEPHARD.egg-info/PKG-INFO
2026-07-27T01:43:34,089   writing dependency_links to SHEPHARD.egg-info/dependency_links.txt
2026-07-27T01:43:34,091   writing requirements to SHEPHARD.egg-info/requires.txt
2026-07-27T01:43:34,093   writing top-level names to SHEPHARD.egg-info/top_level.txt
2026-07-27T01:43:34,126   reading manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-27T01:43:34,133   reading manifest template 'MANIFEST.in'
2026-07-27T01:43:34,142   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2026-07-27T01:43:34,143   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-27T01:43:34,144   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-27T01:43:34,145   adding license file 'LICENSE'
2026-07-27T01:43:34,153   writing manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-27T01:43:34,253   Getting requirements to build wheel: finished with status 'done'
2026-07-27T01:43:34,256   Created temporary directory: /tmp/pip-modern-metadata-xnx1usws
2026-07-27T01:43:34,258   Preparing metadata (pyproject.toml): started
2026-07-27T01:43:34,260   Running command Preparing metadata (pyproject.toml)
2026-07-27T01:43:34,948   running dist_info
2026-07-27T01:43:34,960   creating /tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info
2026-07-27T01:43:34,961   writing /tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info/PKG-INFO
2026-07-27T01:43:34,966   writing dependency_links to /tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info/dependency_links.txt
2026-07-27T01:43:34,968   writing requirements to /tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info/requires.txt
2026-07-27T01:43:34,970   writing top-level names to /tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info/top_level.txt
2026-07-27T01:43:34,972   writing manifest file '/tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info/SOURCES.txt'
2026-07-27T01:43:35,002   reading manifest file '/tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info/SOURCES.txt'
2026-07-27T01:43:35,005   reading manifest template 'MANIFEST.in'
2026-07-27T01:43:35,013   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2026-07-27T01:43:35,014   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-27T01:43:35,016   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-27T01:43:35,016   adding license file 'LICENSE'
2026-07-27T01:43:35,023   writing manifest file '/tmp/pip-modern-metadata-xnx1usws/SHEPHARD.egg-info/SOURCES.txt'
2026-07-27T01:43:35,025   creating '/tmp/pip-modern-metadata-xnx1usws/shephard-0.2.4.dist-info'
2026-07-27T01:43:35,150   Preparing metadata (pyproject.toml): finished with status 'done'
2026-07-27T01:43:35,155   Source in /tmp/pip-wheel-62xu9xnm/shephard_44c092ed97244cb9a273f10ee33800d9 has version 0.2.4, which satisfies requirement shephard==0.2.4 from https://files.pythonhosted.org/packages/4e/a8/d92e021bf1cb6842f6a5b9f2afedcd6ce0f76af18564ff5f0f616b0561eb/shephard-0.2.4.tar.gz
2026-07-27T01:43:35,156   Removed shephard==0.2.4 from https://files.pythonhosted.org/packages/4e/a8/d92e021bf1cb6842f6a5b9f2afedcd6ce0f76af18564ff5f0f616b0561eb/shephard-0.2.4.tar.gz from build tracker '/tmp/pip-build-tracker-yfpmql1q'
2026-07-27T01:43:35,161 Created temporary directory: /tmp/pip-unpack-pnp4r6bb
2026-07-27T01:43:35,162 Building wheels for collected packages: shephard
2026-07-27T01:43:35,166   Created temporary directory: /tmp/pip-wheel-t50y3xmx
2026-07-27T01:43:35,166   Destination directory: /tmp/pip-wheel-t50y3xmx
2026-07-27T01:43:35,168   Building wheel for shephard (pyproject.toml): started
2026-07-27T01:43:35,170   Running command Building wheel for shephard (pyproject.toml)
2026-07-27T01:43:35,842   running bdist_wheel
2026-07-27T01:43:35,864   running build
2026-07-27T01:43:35,864   running build_py
2026-07-27T01:43:35,872   creating build/lib/shephard
2026-07-27T01:43:35,874   copying shephard/sequence_utilities.py -> build/lib/shephard
2026-07-27T01:43:35,876   copying shephard/__init__.py -> build/lib/shephard
2026-07-27T01:43:35,878   copying shephard/exceptions.py -> build/lib/shephard
2026-07-27T01:43:35,880   copying shephard/protein.py -> build/lib/shephard
2026-07-27T01:43:35,884   copying shephard/domain.py -> build/lib/shephard
2026-07-27T01:43:35,887   copying shephard/site.py -> build/lib/shephard
2026-07-27T01:43:35,890   copying shephard/track.py -> build/lib/shephard
2026-07-27T01:43:35,893   copying shephard/_version.py -> build/lib/shephard
2026-07-27T01:43:35,895   copying shephard/general_utilities.py -> build/lib/shephard
2026-07-27T01:43:35,897   copying shephard/proteome.py -> build/lib/shephard
2026-07-27T01:43:35,902   creating build/lib/shephard/tests
2026-07-27T01:43:35,903   copying shephard/tests/test_apis_fasta.py -> build/lib/shephard/tests
2026-07-27T01:43:35,906   copying shephard/tests/test_track_tools.py -> build/lib/shephard/tests
2026-07-27T01:43:35,908   copying shephard/tests/test_api_uniprot_live.py -> build/lib/shephard/tests
2026-07-27T01:43:35,910   copying shephard/tests/test_ProteinAttributesInterface.py -> build/lib/shephard/tests
2026-07-27T01:43:35,912   copying shephard/tests/test_proteome.py -> build/lib/shephard/tests
2026-07-27T01:43:35,915   copying shephard/tests/test_api_albatross.py -> build/lib/shephard/tests
2026-07-27T01:43:35,917   copying shephard/tests/__init__.py -> build/lib/shephard/tests
2026-07-27T01:43:35,919   copying shephard/tests/example_test_function.py -> build/lib/shephard/tests
2026-07-27T01:43:35,921   copying shephard/tests/test_comprehensive_track.py -> build/lib/shephard/tests
2026-07-27T01:43:35,924   copying shephard/tests/test_comprehensive_apis.py -> build/lib/shephard/tests
2026-07-27T01:43:35,926   copying shephard/tests/test_ProteinInterface.py -> build/lib/shephard/tests
2026-07-27T01:43:35,928   copying shephard/tests/test_attribute_tools.py -> build/lib/shephard/tests
2026-07-27T01:43:35,931   copying shephard/tests/test_tracks.py -> build/lib/shephard/tests
2026-07-27T01:43:35,933   copying shephard/tests/test_api_uniprot_annotation.py -> build/lib/shephard/tests
2026-07-27T01:43:35,936   copying shephard/tests/test_si_sites.py -> build/lib/shephard/tests
2026-07-27T01:43:35,938   copying shephard/tests/test_add_remove_annotations.py -> build/lib/shephard/tests
2026-07-27T01:43:35,941   copying shephard/tests/test_protein_site_functions.py -> build/lib/shephard/tests
2026-07-27T01:43:35,943   copying shephard/tests/test_shephard.py -> build/lib/shephard/tests
2026-07-27T01:43:35,945   copying shephard/tests/test_SiteInterface.py -> build/lib/shephard/tests
2026-07-27T01:43:35,947   copying shephard/tests/test_sequence_tools.py -> build/lib/shephard/tests
2026-07-27T01:43:35,949   copying shephard/tests/test_interfaces.py -> build/lib/shephard/tests
2026-07-27T01:43:35,952   copying shephard/tests/test_protein.py -> build/lib/shephard/tests
2026-07-27T01:43:35,954   copying shephard/tests/test_si_domains.py -> build/lib/shephard/tests
2026-07-27T01:43:35,957   copying shephard/tests/test_domains.py -> build/lib/shephard/tests
2026-07-27T01:43:35,959   copying shephard/tests/test_sites.py -> build/lib/shephard/tests
2026-07-27T01:43:35,961   copying shephard/tests/test_bugfix_regressions.py -> build/lib/shephard/tests
2026-07-27T01:43:35,964   copying shephard/tests/test_bugfix_regressions_0_2_3.py -> build/lib/shephard/tests
2026-07-27T01:43:35,967   copying shephard/tests/test_bugfix_regressions_0_2_4.py -> build/lib/shephard/tests
2026-07-27T01:43:35,969   copying shephard/tests/test_comprehensive_interfaces.py -> build/lib/shephard/tests
2026-07-27T01:43:35,972   copying shephard/tests/test_comprehensive_domain.py -> build/lib/shephard/tests
2026-07-27T01:43:35,974   copying shephard/tests/test_comprehensive_site.py -> build/lib/shephard/tests
2026-07-27T01:43:35,977   copying shephard/tests/test_comprehensive_tools.py -> build/lib/shephard/tests
2026-07-27T01:43:35,979   copying shephard/tests/test_comprehensive_proteome.py -> build/lib/shephard/tests
2026-07-27T01:43:35,982   copying shephard/tests/test_api_metapredict.py -> build/lib/shephard/tests
2026-07-27T01:43:35,985   copying shephard/tests/test_comprehensive_protein.py -> build/lib/shephard/tests
2026-07-27T01:43:35,988   copying shephard/tests/test_TrackInterface.py -> build/lib/shephard/tests
2026-07-27T01:43:35,990   copying shephard/tests/test_DomainInterface.py -> build/lib/shephard/tests
2026-07-27T01:43:35,992   copying shephard/tests/test_si_tracks.py -> build/lib/shephard/tests
2026-07-27T01:43:35,995   copying shephard/tests/test_domain_tools.py -> build/lib/shephard/tests
2026-07-27T01:43:35,997   copying shephard/tests/conftest.py -> build/lib/shephard/tests
2026-07-27T01:43:36,000   creating build/lib/shephard/interfaces
2026-07-27T01:43:36,002   copying shephard/interfaces/__init__.py -> build/lib/shephard/interfaces
2026-07-27T01:43:36,004   copying shephard/interfaces/si_protein_attributes.py -> build/lib/shephard/interfaces
2026-07-27T01:43:36,007   copying shephard/interfaces/si_sites.py -> build/lib/shephard/interfaces
2026-07-27T01:43:36,010   copying shephard/interfaces/interface_tools.py -> build/lib/shephard/interfaces
2026-07-27T01:43:36,012   copying shephard/interfaces/si_domains.py -> build/lib/shephard/interfaces
2026-07-27T01:43:36,016   copying shephard/interfaces/si_tracks.py -> build/lib/shephard/interfaces
2026-07-27T01:43:36,019   copying shephard/interfaces/si_proteins.py -> build/lib/shephard/interfaces
2026-07-27T01:43:36,022   creating build/lib/shephard/tools
2026-07-27T01:43:36,023   copying shephard/tools/sequence_tools.py -> build/lib/shephard/tools
2026-07-27T01:43:36,026   copying shephard/tools/__init__.py -> build/lib/shephard/tools
2026-07-27T01:43:36,029   copying shephard/tools/experimental.py -> build/lib/shephard/tools
2026-07-27T01:43:36,032   copying shephard/tools/domain_tools.py -> build/lib/shephard/tools
2026-07-27T01:43:36,035   copying shephard/tools/track_tools.py -> build/lib/shephard/tools
2026-07-27T01:43:36,038   copying shephard/tools/site_tools.py -> build/lib/shephard/tools
2026-07-27T01:43:36,040   copying shephard/tools/attribute_tools.py -> build/lib/shephard/tools
2026-07-27T01:43:36,043   creating build/lib/shephard/apis
2026-07-27T01:43:36,044   copying shephard/apis/uniprot.py -> build/lib/shephard/apis
2026-07-27T01:43:36,048   copying shephard/apis/__init__.py -> build/lib/shephard/apis
2026-07-27T01:43:36,050   copying shephard/apis/albatross_api.py -> build/lib/shephard/apis
2026-07-27T01:43:36,053   copying shephard/apis/metapredict_api.py -> build/lib/shephard/apis
2026-07-27T01:43:36,055   copying shephard/apis/fasta.py -> build/lib/shephard/apis
2026-07-27T01:43:36,059   running egg_info
2026-07-27T01:43:36,071   writing SHEPHARD.egg-info/PKG-INFO
2026-07-27T01:43:36,075   writing dependency_links to SHEPHARD.egg-info/dependency_links.txt
2026-07-27T01:43:36,077   writing requirements to SHEPHARD.egg-info/requires.txt
2026-07-27T01:43:36,078   writing top-level names to SHEPHARD.egg-info/top_level.txt
2026-07-27T01:43:36,098   reading manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-27T01:43:36,105   reading manifest template 'MANIFEST.in'
2026-07-27T01:43:36,114   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2026-07-27T01:43:36,116   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-27T01:43:36,117   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-27T01:43:36,118   adding license file 'LICENSE'
2026-07-27T01:43:36,126   writing manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-27T01:43:36,137   copying shephard/.DS_Store -> build/lib/shephard
2026-07-27T01:43:36,140   copying shephard/py.typed -> build/lib/shephard
2026-07-27T01:43:36,142   creating build/lib/shephard/data
2026-07-27T01:43:36,143   copying shephard/data/README.md -> build/lib/shephard/data
2026-07-27T01:43:36,146   copying shephard/data/look_and_say.dat -> build/lib/shephard/data
2026-07-27T01:43:36,148   creating build/lib/shephard/data/test_data
2026-07-27T01:43:36,149   copying shephard/data/test_data/testset_1.fasta.fai -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,152   copying shephard/data/test_data/TS1_domains_idr.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,154   copying shephard/data/test_data/TS1_protein_attributes.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,157   copying shephard/data/test_data/TS1_sites.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,159   copying shephard/data/test_data/ts1_bonus_sites.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,162   copying shephard/data/test_data/testset_1_ptms.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,164   copying shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,166   copying shephard/data/test_data/TS1_domains_pscore.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,169   copying shephard/data/test_data/TS1_tracks_pscore.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,172   copying shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,174   copying shephard/data/test_data/testset_1.fasta -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,177   copying shephard/data/test_data/TS1_small_proteins.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,179   copying shephard/data/test_data/seqs.fasta -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,182   copying shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,185   copying shephard/data/test_data/names.txt -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,187   copying shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/lib/shephard/data/test_data
2026-07-27T01:43:36,189   copying shephard/tests/test_scratchpad.ipynb -> build/lib/shephard/tests
2026-07-27T01:43:36,192   creating build/lib/shephard/tests/.ipynb_checkpoints
2026-07-27T01:43:36,194   copying shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/lib/shephard/tests/.ipynb_checkpoints
2026-07-27T01:43:36,196   copying shephard/tools/attribute_tools.py~ -> build/lib/shephard/tools
2026-07-27T01:43:36,199   creating build/lib/shephard/tests/output_test
2026-07-27T01:43:36,200   copying shephard/tests/output_test/all_symbols_test.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,203   copying shephard/tests/output_test/all_values_test.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,206   copying shephard/tests/output_test/all_values_test_from_list.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,209   copying shephard/tests/output_test/out_tracks.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,213   copying shephard/tests/output_test/readme.md -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,214   copying shephard/tests/output_test/shephard_track_phosres.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,217   copying shephard/tests/output_test/shephard_track_pscore.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,219   copying shephard/tests/output_test/test_domains.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,221   copying shephard/tests/output_test/test_domains_types.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,223   copying shephard/tests/output_test/test_sites.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,227   copying shephard/tests/output_test/track_phospho_track.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,228   copying shephard/tests/output_test/track_random_vals.tsv -> build/lib/shephard/tests/output_test
2026-07-27T01:43:36,252   installing to build/bdist.linux-armv7l/wheel
2026-07-27T01:43:36,253   running install
2026-07-27T01:43:36,276   running install_lib
2026-07-27T01:43:36,283   creating build/bdist.linux-armv7l/wheel
2026-07-27T01:43:36,285   creating build/bdist.linux-armv7l/wheel/shephard
2026-07-27T01:43:36,286   copying build/lib/shephard/sequence_utilities.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,289   creating build/bdist.linux-armv7l/wheel/shephard/tests
2026-07-27T01:43:36,290   copying build/lib/shephard/tests/test_apis_fasta.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,292   copying build/lib/shephard/tests/test_track_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,294   copying build/lib/shephard/tests/test_scratchpad.ipynb -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,296   copying build/lib/shephard/tests/test_api_uniprot_live.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,298   copying build/lib/shephard/tests/test_ProteinAttributesInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,300   copying build/lib/shephard/tests/test_proteome.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,302   copying build/lib/shephard/tests/test_api_albatross.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,304   copying build/lib/shephard/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,306   copying build/lib/shephard/tests/example_test_function.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,308   copying build/lib/shephard/tests/test_comprehensive_track.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,311   creating build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2026-07-27T01:43:36,312   copying build/lib/shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/bdist.linux-armv7l/wheel/./shephard/tests/.ipynb_checkpoints
2026-07-27T01:43:36,314   copying build/lib/shephard/tests/test_comprehensive_apis.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,316   copying build/lib/shephard/tests/test_ProteinInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,318   copying build/lib/shephard/tests/test_attribute_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,319   copying build/lib/shephard/tests/test_tracks.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,321   copying build/lib/shephard/tests/test_api_uniprot_annotation.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,324   copying build/lib/shephard/tests/test_si_sites.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,326   copying build/lib/shephard/tests/test_add_remove_annotations.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,328   copying build/lib/shephard/tests/test_protein_site_functions.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,330   copying build/lib/shephard/tests/test_shephard.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,331   copying build/lib/shephard/tests/test_SiteInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,333   copying build/lib/shephard/tests/test_sequence_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,335   copying build/lib/shephard/tests/test_interfaces.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,336   copying build/lib/shephard/tests/test_protein.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,338   copying build/lib/shephard/tests/test_si_domains.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,340   copying build/lib/shephard/tests/test_domains.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,343   copying build/lib/shephard/tests/test_sites.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,344   copying build/lib/shephard/tests/test_bugfix_regressions.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,346   copying build/lib/shephard/tests/test_bugfix_regressions_0_2_3.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,349   copying build/lib/shephard/tests/test_bugfix_regressions_0_2_4.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,351   copying build/lib/shephard/tests/test_comprehensive_interfaces.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,353   copying build/lib/shephard/tests/test_comprehensive_domain.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,355   copying build/lib/shephard/tests/test_comprehensive_site.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,358   copying build/lib/shephard/tests/test_comprehensive_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,360   copying build/lib/shephard/tests/test_comprehensive_proteome.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,362   copying build/lib/shephard/tests/test_api_metapredict.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,364   copying build/lib/shephard/tests/test_comprehensive_protein.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,367   creating build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2026-07-27T01:43:36,368   copying build/lib/shephard/tests/output_test/track_random_vals.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,371   copying build/lib/shephard/tests/output_test/shephard_track_pscore.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,373   copying build/lib/shephard/tests/output_test/all_values_test_from_list.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,376   copying build/lib/shephard/tests/output_test/test_domains_types.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,377   copying build/lib/shephard/tests/output_test/all_symbols_test.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,379   copying build/lib/shephard/tests/output_test/test_sites.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,382   copying build/lib/shephard/tests/output_test/test_domains.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,384   copying build/lib/shephard/tests/output_test/track_phospho_track.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,385   copying build/lib/shephard/tests/output_test/shephard_track_phosres.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,387   copying build/lib/shephard/tests/output_test/out_tracks.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,390   copying build/lib/shephard/tests/output_test/all_values_test.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,392   copying build/lib/shephard/tests/output_test/readme.md -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-27T01:43:36,394   copying build/lib/shephard/tests/test_TrackInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,396   copying build/lib/shephard/tests/test_DomainInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,397   copying build/lib/shephard/tests/test_si_tracks.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,399   copying build/lib/shephard/tests/test_domain_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,402   copying build/lib/shephard/tests/conftest.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-27T01:43:36,404   creating build/bdist.linux-armv7l/wheel/shephard/interfaces
2026-07-27T01:43:36,405   copying build/lib/shephard/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-27T01:43:36,407   copying build/lib/shephard/interfaces/si_protein_attributes.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-27T01:43:36,409   copying build/lib/shephard/interfaces/si_sites.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-27T01:43:36,412   copying build/lib/shephard/interfaces/interface_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-27T01:43:36,414   copying build/lib/shephard/interfaces/si_domains.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-27T01:43:36,417   copying build/lib/shephard/interfaces/si_tracks.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-27T01:43:36,419   copying build/lib/shephard/interfaces/si_proteins.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-27T01:43:36,422   copying build/lib/shephard/.DS_Store -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,424   copying build/lib/shephard/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,426   copying build/lib/shephard/exceptions.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,427   copying build/lib/shephard/protein.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,431   copying build/lib/shephard/domain.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,433   copying build/lib/shephard/site.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,436   copying build/lib/shephard/track.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,439   creating build/bdist.linux-armv7l/wheel/shephard/tools
2026-07-27T01:43:36,440   copying build/lib/shephard/tools/sequence_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,442   copying build/lib/shephard/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,444   copying build/lib/shephard/tools/experimental.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,446   copying build/lib/shephard/tools/domain_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,448   copying build/lib/shephard/tools/track_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,450   copying build/lib/shephard/tools/attribute_tools.py~ -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,452   copying build/lib/shephard/tools/site_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,454   copying build/lib/shephard/tools/attribute_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-27T01:43:36,455   copying build/lib/shephard/_version.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,457   creating build/bdist.linux-armv7l/wheel/shephard/apis
2026-07-27T01:43:36,458   copying build/lib/shephard/apis/uniprot.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-27T01:43:36,461   copying build/lib/shephard/apis/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-27T01:43:36,463   copying build/lib/shephard/apis/albatross_api.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-27T01:43:36,465   copying build/lib/shephard/apis/metapredict_api.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-27T01:43:36,467   copying build/lib/shephard/apis/fasta.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-27T01:43:36,470   copying build/lib/shephard/general_utilities.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,472   creating build/bdist.linux-armv7l/wheel/shephard/data
2026-07-27T01:43:36,473   copying build/lib/shephard/data/README.md -> build/bdist.linux-armv7l/wheel/./shephard/data
2026-07-27T01:43:36,475   creating build/bdist.linux-armv7l/wheel/shephard/data/test_data
2026-07-27T01:43:36,476   copying build/lib/shephard/data/test_data/testset_1.fasta.fai -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,478   copying build/lib/shephard/data/test_data/TS1_domains_idr.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,480   copying build/lib/shephard/data/test_data/TS1_protein_attributes.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,482   copying build/lib/shephard/data/test_data/TS1_sites.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,484   copying build/lib/shephard/data/test_data/ts1_bonus_sites.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,485   copying build/lib/shephard/data/test_data/testset_1_ptms.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,487   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,489   copying build/lib/shephard/data/test_data/TS1_domains_pscore.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,491   copying build/lib/shephard/data/test_data/TS1_tracks_pscore.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,493   copying build/lib/shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,495   copying build/lib/shephard/data/test_data/testset_1.fasta -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,497   copying build/lib/shephard/data/test_data/TS1_small_proteins.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,499   copying build/lib/shephard/data/test_data/seqs.fasta -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,501   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,503   copying build/lib/shephard/data/test_data/names.txt -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,504   copying build/lib/shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-27T01:43:36,506   copying build/lib/shephard/data/look_and_say.dat -> build/bdist.linux-armv7l/wheel/./shephard/data
2026-07-27T01:43:36,508   copying build/lib/shephard/proteome.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,511   copying build/lib/shephard/py.typed -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-27T01:43:36,512   running install_egg_info
2026-07-27T01:43:36,518   Copying SHEPHARD.egg-info to build/bdist.linux-armv7l/wheel/./SHEPHARD-0.2.4-py3.11.egg-info
2026-07-27T01:43:36,529   running install_scripts
2026-07-27T01:43:36,539   creating build/bdist.linux-armv7l/wheel/shephard-0.2.4.dist-info/WHEEL
2026-07-27T01:43:36,541   creating '/tmp/pip-wheel-t50y3xmx/.tmp-6sra9w5c/shephard-0.2.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-07-27T01:43:36,544   adding 'shephard/.DS_Store'
2026-07-27T01:43:36,545   adding 'shephard/__init__.py'
2026-07-27T01:43:36,547   adding 'shephard/_version.py'
2026-07-27T01:43:36,549   adding 'shephard/domain.py'
2026-07-27T01:43:36,551   adding 'shephard/exceptions.py'
2026-07-27T01:43:36,552   adding 'shephard/general_utilities.py'
2026-07-27T01:43:36,562   adding 'shephard/protein.py'
2026-07-27T01:43:36,568   adding 'shephard/proteome.py'
2026-07-27T01:43:36,570   adding 'shephard/py.typed'
2026-07-27T01:43:36,571   adding 'shephard/sequence_utilities.py'
2026-07-27T01:43:36,573   adding 'shephard/site.py'
2026-07-27T01:43:36,575   adding 'shephard/track.py'
2026-07-27T01:43:36,577   adding 'shephard/apis/__init__.py'
2026-07-27T01:43:36,578   adding 'shephard/apis/albatross_api.py'
2026-07-27T01:43:36,581   adding 'shephard/apis/fasta.py'
2026-07-27T01:43:36,583   adding 'shephard/apis/metapredict_api.py'
2026-07-27T01:43:36,591   adding 'shephard/apis/uniprot.py'
2026-07-27T01:43:36,593   adding 'shephard/data/README.md'
2026-07-27T01:43:36,594   adding 'shephard/data/look_and_say.dat'
2026-07-27T01:43:36,595   adding 'shephard/data/test_data/TS1_domains_idr.tsv'
2026-07-27T01:43:36,597   adding 'shephard/data/test_data/TS1_domains_idr_and_others.tsv'
2026-07-27T01:43:36,598   adding 'shephard/data/test_data/TS1_domains_pscore.tsv'
2026-07-27T01:43:36,599   adding 'shephard/data/test_data/TS1_protein_attributes.tsv'
2026-07-27T01:43:36,600   adding 'shephard/data/test_data/TS1_protein_attributes_several.tsv'
2026-07-27T01:43:36,602   adding 'shephard/data/test_data/TS1_sites.tsv'
2026-07-27T01:43:36,603   adding 'shephard/data/test_data/TS1_small_proteins.tsv'
2026-07-27T01:43:36,611   adding 'shephard/data/test_data/TS1_tracks_pscore.tsv'
2026-07-27T01:43:36,613   adding 'shephard/data/test_data/names.txt'
2026-07-27T01:43:36,614   adding 'shephard/data/test_data/seqs.fasta'
2026-07-27T01:43:36,616   adding 'shephard/data/test_data/testset_1.fasta'
2026-07-27T01:43:36,617   adding 'shephard/data/test_data/testset_1.fasta.fai'
2026-07-27T01:43:36,618   adding 'shephard/data/test_data/testset_1_ptms.tsv'
2026-07-27T01:43:36,619   adding 'shephard/data/test_data/ts1_bonus_sites.tsv'
2026-07-27T01:43:36,621   adding 'shephard/data/test_data/ts1_bonus_sites_bad.tsv'
2026-07-27T01:43:36,622   adding 'shephard/data/test_data/ts1_bonus_sites_bad2.tsv'
2026-07-27T01:43:36,624   adding 'shephard/interfaces/__init__.py'
2026-07-27T01:43:36,625   adding 'shephard/interfaces/interface_tools.py'
2026-07-27T01:43:36,629   adding 'shephard/interfaces/si_domains.py'
2026-07-27T01:43:36,631   adding 'shephard/interfaces/si_protein_attributes.py'
2026-07-27T01:43:36,634   adding 'shephard/interfaces/si_proteins.py'
2026-07-27T01:43:36,636   adding 'shephard/interfaces/si_sites.py'
2026-07-27T01:43:36,640   adding 'shephard/interfaces/si_tracks.py'
2026-07-27T01:43:36,643   adding 'shephard/tests/__init__.py'
2026-07-27T01:43:36,644   adding 'shephard/tests/conftest.py'
2026-07-27T01:43:36,645   adding 'shephard/tests/example_test_function.py'
2026-07-27T01:43:36,647   adding 'shephard/tests/test_DomainInterface.py'
2026-07-27T01:43:36,648   adding 'shephard/tests/test_ProteinAttributesInterface.py'
2026-07-27T01:43:36,649   adding 'shephard/tests/test_ProteinInterface.py'
2026-07-27T01:43:36,650   adding 'shephard/tests/test_SiteInterface.py'
2026-07-27T01:43:36,652   adding 'shephard/tests/test_TrackInterface.py'
2026-07-27T01:43:36,653   adding 'shephard/tests/test_add_remove_annotations.py'
2026-07-27T01:43:36,654   adding 'shephard/tests/test_api_albatross.py'
2026-07-27T01:43:36,656   adding 'shephard/tests/test_api_metapredict.py'
2026-07-27T01:43:36,660   adding 'shephard/tests/test_api_uniprot_annotation.py'
2026-07-27T01:43:36,661   adding 'shephard/tests/test_api_uniprot_live.py'
2026-07-27T01:43:36,663   adding 'shephard/tests/test_apis_fasta.py'
2026-07-27T01:43:36,664   adding 'shephard/tests/test_attribute_tools.py'
2026-07-27T01:43:36,666   adding 'shephard/tests/test_bugfix_regressions.py'
2026-07-27T01:43:36,668   adding 'shephard/tests/test_bugfix_regressions_0_2_3.py'
2026-07-27T01:43:36,670   adding 'shephard/tests/test_bugfix_regressions_0_2_4.py'
2026-07-27T01:43:36,672   adding 'shephard/tests/test_comprehensive_apis.py'
2026-07-27T01:43:36,673   adding 'shephard/tests/test_comprehensive_domain.py'
2026-07-27T01:43:36,676   adding 'shephard/tests/test_comprehensive_interfaces.py'
2026-07-27T01:43:36,678   adding 'shephard/tests/test_comprehensive_protein.py'
2026-07-27T01:43:36,680   adding 'shephard/tests/test_comprehensive_proteome.py'
2026-07-27T01:43:36,681   adding 'shephard/tests/test_comprehensive_site.py'
2026-07-27T01:43:36,683   adding 'shephard/tests/test_comprehensive_tools.py'
2026-07-27T01:43:36,685   adding 'shephard/tests/test_comprehensive_track.py'
2026-07-27T01:43:36,686   adding 'shephard/tests/test_domain_tools.py'
2026-07-27T01:43:36,688   adding 'shephard/tests/test_domains.py'
2026-07-27T01:43:36,689   adding 'shephard/tests/test_interfaces.py'
2026-07-27T01:43:36,691   adding 'shephard/tests/test_protein.py'
2026-07-27T01:43:36,693   adding 'shephard/tests/test_protein_site_functions.py'
2026-07-27T01:43:36,694   adding 'shephard/tests/test_proteome.py'
2026-07-27T01:43:36,697   adding 'shephard/tests/test_scratchpad.ipynb'
2026-07-27T01:43:36,698   adding 'shephard/tests/test_sequence_tools.py'
2026-07-27T01:43:36,699   adding 'shephard/tests/test_shephard.py'
2026-07-27T01:43:36,701   adding 'shephard/tests/test_si_domains.py'
2026-07-27T01:43:36,703   adding 'shephard/tests/test_si_sites.py'
2026-07-27T01:43:36,704   adding 'shephard/tests/test_si_tracks.py'
2026-07-27T01:43:36,706   adding 'shephard/tests/test_sites.py'
2026-07-27T01:43:36,707   adding 'shephard/tests/test_track_tools.py'
2026-07-27T01:43:36,708   adding 'shephard/tests/test_tracks.py'
2026-07-27T01:43:36,710   adding 'shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb'
2026-07-27T01:43:36,712   adding 'shephard/tests/output_test/all_symbols_test.tsv'
2026-07-27T01:43:36,714   adding 'shephard/tests/output_test/all_values_test.tsv'
2026-07-27T01:43:36,716   adding 'shephard/tests/output_test/all_values_test_from_list.tsv'
2026-07-27T01:43:36,725   adding 'shephard/tests/output_test/out_tracks.tsv'
2026-07-27T01:43:36,726   adding 'shephard/tests/output_test/readme.md'
2026-07-27T01:43:36,728   adding 'shephard/tests/output_test/shephard_track_phosres.tsv'
2026-07-27T01:43:36,736   adding 'shephard/tests/output_test/shephard_track_pscore.tsv'
2026-07-27T01:43:36,737   adding 'shephard/tests/output_test/test_domains.tsv'
2026-07-27T01:43:36,739   adding 'shephard/tests/output_test/test_domains_types.tsv'
2026-07-27T01:43:36,742   adding 'shephard/tests/output_test/test_sites.tsv'
2026-07-27T01:43:36,743   adding 'shephard/tests/output_test/track_phospho_track.tsv'
2026-07-27T01:43:36,745   adding 'shephard/tests/output_test/track_random_vals.tsv'
2026-07-27T01:43:36,747   adding 'shephard/tools/__init__.py'
2026-07-27T01:43:36,748   adding 'shephard/tools/attribute_tools.py'
2026-07-27T01:43:36,750   adding 'shephard/tools/attribute_tools.py~'
2026-07-27T01:43:36,752   adding 'shephard/tools/domain_tools.py'
2026-07-27T01:43:36,754   adding 'shephard/tools/experimental.py'
2026-07-27T01:43:36,756   adding 'shephard/tools/sequence_tools.py'
2026-07-27T01:43:36,757   adding 'shephard/tools/site_tools.py'
2026-07-27T01:43:36,759   adding 'shephard/tools/track_tools.py'
2026-07-27T01:43:36,762   adding 'shephard-0.2.4.dist-info/licenses/LICENSE'
2026-07-27T01:43:36,763   adding 'shephard-0.2.4.dist-info/METADATA'
2026-07-27T01:43:36,764   adding 'shephard-0.2.4.dist-info/WHEEL'
2026-07-27T01:43:36,765   adding 'shephard-0.2.4.dist-info/top_level.txt'
2026-07-27T01:43:36,767   adding 'shephard-0.2.4.dist-info/RECORD'
2026-07-27T01:43:36,773   removing build/bdist.linux-armv7l/wheel
2026-07-27T01:43:36,899   Building wheel for shephard (pyproject.toml): finished with status 'done'
2026-07-27T01:43:36,908   Created wheel for shephard: filename=shephard-0.2.4-py3-none-any.whl size=263038 sha256=d5035e244b17e2bc8dc76c4b199d038742ea2cd90ad3206954ad8a3b0db20a57
2026-07-27T01:43:36,910   Stored in directory: /tmp/pip-ephem-wheel-cache-5l_vq8s8/wheels/08/43/a0/bdb5bcef97f248d4a9c55062580c04b4728c56682c9f8d4e67
2026-07-27T01:43:36,923 Successfully built shephard
2026-07-27T01:43:36,936 Removed build tracker: '/tmp/pip-build-tracker-yfpmql1q'